I have a fascination in biology and have wondered how proteins designed to make certain molecules like DNA or ATP, etc., create the chemical bonds between the atoms when making it.
I understand that they don’t make them from scratch, they usual just “smash” two different molecules together, but still how are the bonds created?
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Proteins can exploit some tricks of chemistry to make a chemical reaction more like to happen. This is usually due to the shape of the protein; it might be able to “hold” the two component molecules in just the right way that they can react together. Meanwhile, if the two molecules were just floating around willy-nilly, it would take a lot of time before they happened to contact each other in that particular way to allow the reaction to occur.
In this sense, proteins create additional chances for the molecules to react; they’re not causing the chemical reaction to happen as much as making it easier for it to happen.
Proteins are [mostly] stitched together by a molecule called a ribosome.
Ribosomes add amino acids one by one to a long chain called a polypeptide. Proteins are made of one or more polypeptides, sometimes with modifications made later.
The ribosome grabs the appropriate amino acid from the cytoplasm (“stuff inside the cell”) and adds it through a condensation reaction involving the -OH off of the carboxylic acid end of one amino acid and the hydrogen off of the nitrogen end of the other.
The actual mechanism by which this happens is complicated, but, yeah, mostly the ribosome brings the ends close together. What probably happens is something like:
The oxygen in the -OH group is close to one of the hydrogens hanging off of the nitrogen. If they’re close enough, the oxygen will start to grab at the hydrogen more than the nitrogen does. Once the oxygen grabs that hydrogen, it now has two hydrogens and decides that it would rather be a water molecule by itself than hang around with the lame amino acid. This leaves the carbon that oxygen used to be bonded to sad and alone. Meanwhile, the nitrogen that just lost its hydrogen is also sad and alone. The carbon and nitrogen find comfort in each other, and form a lasting bond. Meanwhile, the water goes away, maybe to find itself in Bali or something.
I’m just now realizing you asked how proteins make DNA, not how DNA makes proteins.
Anyway, it’s similar: the protein grabs the two molecules to be bonded, and put them close to each other. If they’re placed close to each other at the right orientation, then they’ll start to reaction and form a bond. Sometimes the protein may also change shape while the reaction proceeds, helping force it in a particular direction, and sometimes the protein might include a metal atom which sort of helps the electrons move from one place to another as the bond forms.
Okay so I’m going to start off by talking about energy levels. [This is a graph ](https://images.app.goo.gl/ezSTotb9KEEg1TFD9)of the energy states associated with an exothermic reaction, or a reaction that releases energy. We start with the reactants, which then form a transition state of higher energy, then they settle down into the lower energy products. The key here is that the transition state requires energy to be put in to reach, and we chemists call this the activation energy. Any catalyst, protein or not, works by reducing the amount of activation energy a reactions requires.
So what does this have to do with proteins? Well, the way protein enzymes work is by having a binding affinity not just to the reactants but to THEIR TRANSITION STATE; which means the reactants binding to the enzyme “prepares” the reactants for the upcoming reaction and makes it far easier for the desired reaction to happen. Sometimes, this is a simple as literally squishing two reactants close enough together that they react.
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